protk 1.1.9 → 1.1.10
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- data/lib/protk/constants.rb +1 -1
- data/lib/protk/data/apt-get_packages.yaml +4 -4
- data/lib/protk/setup_rakefile.rake +17 -13
- metadata +1 -1
data/lib/protk/constants.rb
CHANGED
@@ -244,7 +244,7 @@ class Constants
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244
244
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user_config_yml = YAML.load_file "#{self.protk_dir}/config.yml" if File.exist? "#{self.protk_dir}/config.yml"
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245
245
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246
246
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if ( user_config_yml !=nil )
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247
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-
dict =
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247
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+
dict = user_config_yml.merge dict
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248
248
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end
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249
249
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250
250
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File.open("#{self.protk_dir}/config.yml", "w") {|file| file.puts(dict.to_yaml) }
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@@ -10,9 +10,6 @@ rvm:
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10
10
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- openssl
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11
11
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- libreadline6
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12
12
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- libreadline6-dev
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13
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-
- openssl
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14
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-
- libreadline6
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15
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-
- libreadline6-dev
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16
13
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- git-core
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17
14
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- zlib1g
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18
15
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- zlib1g-dev
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@@ -26,11 +23,14 @@ rvm:
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26
23
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- subversion
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27
24
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- pkg-config
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28
25
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26
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+
protk:
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27
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+
- libxml2-dev
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28
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+
- libxml2
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29
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+
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29
30
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galaxy:
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30
31
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- mercurial
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31
32
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32
33
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tpp:
|
33
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-
- cpanminus
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34
34
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- g++
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35
35
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- subversion
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36
36
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- libbz2-dev
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@@ -34,9 +34,12 @@ def download_buildfile url, file
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|
34
34
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end
|
35
35
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|
36
36
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def download_task url, packagefile
|
37
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-
file "#{@download_dir}/#{packagefile}" => @download_dir do
|
37
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+
file "#{@download_dir}/#{packagefile}" => @download_dir do
|
38
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+
p "Downloading from #{url}"
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38
39
|
download_buildfile "#{url}", "#{packagefile}"
|
40
|
+
p "Done"
|
39
41
|
end
|
42
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+
"#{@download_dir}/#{packagefile}"
|
40
43
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end
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41
44
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|
42
45
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#
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@@ -94,12 +97,13 @@ perl_locallib_version="1.008004"
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94
97
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perl_locallib_packagefile="local-lib-#{perl_locallib_version}.tar.gz"
|
95
98
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perl_locallib_installed_file = "#{env.protk_dir}/perl5/lib/perl5/local/lib.pm"
|
96
99
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perl_locallib_url = "http://search.cpan.org/CPAN/authors/id/A/AP/APEIRON/local-lib-#{perl_locallib_version}.tar.gz"
|
100
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+
perl_dir = "#{env.protk_dir}/perl5"
|
97
101
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|
98
102
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download_task perl_locallib_url, perl_locallib_packagefile
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99
103
|
|
100
104
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file perl_locallib_installed_file => [@build_dir,"#{@download_dir}/#{perl_locallib_packagefile}"] do
|
101
105
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sh %{cp #{@download_dir}/#{perl_locallib_packagefile} #{@build_dir}}
|
102
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-
|
106
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+
|
103
107
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|
104
108
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sh %{cd #{@build_dir}; gunzip -f local-lib-#{perl_locallib_version}.tar.gz }
|
105
109
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sh %{cd #{@build_dir}; tar -xf local-lib-#{perl_locallib_version}.tar }
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@@ -107,13 +111,13 @@ file perl_locallib_installed_file => [@build_dir,"#{@download_dir}/#{perl_local
|
|
107
111
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# clean_build_dir if ok
|
108
112
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end
|
109
113
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|
110
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-
if !Pathname.new("~/.bashrc").exist? || File.read("~/.bashrc") =~ /Mlocal::lib/
|
111
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-
|
112
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-
end
|
114
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+
# if !Pathname.new("~/.bashrc").exist? || File.read("~/.bashrc") =~ /Mlocal::lib/
|
115
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+
# sh "echo 'eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir})' >>~/.bashrc"
|
116
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+
# end
|
113
117
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|
114
|
-
if !Pathname.new("~/.bash_profile").exist? || File.read("~/.bash_profile") =~ /Mlocal::lib/
|
115
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-
|
116
|
-
end
|
118
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+
# if !Pathname.new("~/.bash_profile").exist? || File.read("~/.bash_profile") =~ /Mlocal::lib/
|
119
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+
# sh "echo 'eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir})' >>~/.bash_profile"
|
120
|
+
# end
|
117
121
|
|
118
122
|
sh "eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir});curl -L http://cpanmin.us | perl - --self-upgrade"
|
119
123
|
end
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@@ -134,13 +138,13 @@ tpp_packagefile="TPP-#{tpp_version}.tgz"
|
|
134
138
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tpp_installed_file = "#{env.xinteract}"
|
135
139
|
tpp_url = "https://dl.dropbox.com/u/226794/TPP-4.6.1.tgz"
|
136
140
|
|
137
|
-
download_task tpp_url, tpp_packagefile
|
141
|
+
tpp_download_file = download_task tpp_url, tpp_packagefile
|
138
142
|
|
139
143
|
# Build
|
140
|
-
file tpp_installed_file => [:perl_locallib,@build_dir,
|
144
|
+
file tpp_installed_file => [:perl_locallib,@build_dir,tpp_download_file] do
|
141
145
|
sh %{cp #{@download_dir}/#{tpp_packagefile} #{@build_dir}}
|
142
|
-
sh %{cpanm --local-lib=#{env.protk_dir}/perl5 XML::Parser}
|
143
|
-
sh %{cpanm --local-lib=#{env.protk_dir}/perl5 CGI --force}
|
146
|
+
sh %{eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir});cpanm --local-lib=#{env.protk_dir}/perl5 XML::Parser}
|
147
|
+
sh %{eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir});cpanm --local-lib=#{env.protk_dir}/perl5 CGI --force}
|
144
148
|
|
145
149
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sh %{cd #{@build_dir};tar -xvzf TPP-#{tpp_version}.tgz}
|
146
150
|
|
@@ -168,7 +172,7 @@ file tpp_installed_file => [:perl_locallib,@build_dir,"#{@download_dir}/#{tpp_pa
|
|
168
172
|
f.write subs_text
|
169
173
|
end
|
170
174
|
end
|
171
|
-
sh %{cd #{@build_dir}/TPP-#{tpp_version}/trans_proteomic_pipeline/src ; make; make install}
|
175
|
+
sh %{eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir});cd #{@build_dir}/TPP-#{tpp_version}/trans_proteomic_pipeline/src ; make; make install}
|
172
176
|
|
173
177
|
end
|
174
178
|
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